ICTV at the Paris ICV: Results of the Plenary Session and the Binomial Ballot
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Kitahara Et at AVIROL.Pdf
Title A unique mitovirus from Glomeromycota, the phylum of arbuscular mycorrhizal fungi Author(s) Kitahara, Ryoko; Ikeda, Yoji; Shimura, Hanako; Masuta, Chikara; Ezawa, Tatsuhiro Archives of Virology, 159(8), 2157-2160 Citation https://doi.org/10.1007/s00705-014-1999-1 Issue Date 2014-08 Doc URL http://hdl.handle.net/2115/59807 Rights The final publication is available at Springer via http://dx.doi.org/10.1007/s00705-014-1999-1 Type article (author version) File Information Kitahara_et_at_AVIROL.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Arch Virol, accepted for publication: Jan 21 2014 DOI: 10.1007/s00705-014-1999-1 Title: A unique mitovirus from Glomeromycota, the phylum of arbuscular mycorrhizal fungi Authors: Ryoko Kitahara, Yoji Ikeda, Hanako Shimura, Chikara Masuta, and Tatsuhiro Ezawa*. Address: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589 Japan Authors for correspondence: Tatsuhiro Ezawa Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589 Japan Tel +81-11-706-3845; Fax +81-11-706-3845 Email [email protected] No. of table: N/A No. of figure: two No. of color figure for online publication: one (Fig. 1) Supplementary information: three figures and one table Kitahara et al. 1 Abstract 2 3 Arbuscular mycorrhizal (AM) fungi that belong to the phylum Glomeromycota associate 4 with most land plants and supply mineral nutrients to the host plants. One of the four viral 5 segments found by deep-sequencing of dsRNA in the AM fungus Rhizophagus clarus strain 6 RF1 showed similarity to mitoviruses and is characterized in this report. -
Virus Particle Structures
Virus Particle Structures Virus Particle Structures Palmenberg, A.C. and Sgro, J.-Y. COLOR PLATE LEGENDS These color plates depict the relative sizes and comparative virion structures of multiple types of viruses. The renderings are based on data from published atomic coordinates as determined by X-ray crystallography. The international online repository for 3D coordinates is the Protein Databank (www.rcsb.org/pdb/), maintained by the Research Collaboratory for Structural Bioinformatics (RCSB). The VIPER web site (mmtsb.scripps.edu/viper), maintains a parallel collection of PDB coordinates for icosahedral viruses and additionally offers a version of each data file permuted into the same relative 3D orientation (Reddy, V., Natarajan, P., Okerberg, B., Li, K., Damodaran, K., Morton, R., Brooks, C. and Johnson, J. (2001). J. Virol., 75, 11943-11947). VIPER also contains an excellent repository of instructional materials pertaining to icosahedral symmetry and viral structures. All images presented here, except for the filamentous viruses, used the standard VIPER orientation along the icosahedral 2-fold axis. With the exception of Plate 3 as described below, these images were generated from their atomic coordinates using a novel radial depth-cue colorization technique and the program Rasmol (Sayle, R.A., Milner-White, E.J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem Sci., 20, 374-376). First, the Temperature Factor column for every atom in a PDB coordinate file was edited to record a measure of the radial distance from the virion center. The files were rendered using the Rasmol spacefill menu, with specular and shadow options according to the Van de Waals radius of each atom. -
Genetic Content and Evolution of Adenoviruses Andrew J
Journal of General Virology (2003), 84, 2895–2908 DOI 10.1099/vir.0.19497-0 Review Genetic content and evolution of adenoviruses Andrew J. Davison,1 Ma´ria Benko´´ 2 and Bala´zs Harrach2 Correspondence 1MRC Virology Unit, Institute of Virology, Church Street, Glasgow G11 5JR, UK Andrew Davison 2Veterinary Medical Research Institute, Hungarian Academy of Sciences, H-1581 Budapest, [email protected] Hungary This review provides an update of the genetic content, phylogeny and evolution of the family Adenoviridae. An appraisal of the condition of adenovirus genomics highlights the need to ensure that public sequence information is interpreted accurately. To this end, all complete genome sequences available have been reannotated. Adenoviruses fall into four recognized genera, plus possibly a fifth, which have apparently evolved with their vertebrate hosts, but have also engaged in a number of interspecies transmission events. Genes inherited by all modern adenoviruses from their common ancestor are located centrally in the genome and are involved in replication and packaging of viral DNA and formation and structure of the virion. Additional niche-specific genes have accumulated in each lineage, mostly near the genome termini. Capture and duplication of genes in the setting of a ‘leader–exon structure’, which results from widespread use of splicing, appear to have been central to adenovirus evolution. The antiquity of the pre-vertebrate lineages that ultimately gave rise to the Adenoviridae is illustrated by morphological similarities between adenoviruses and bacteriophages, and by use of a protein-primed DNA replication strategy by adenoviruses, certain bacteria and bacteriophages, and linear plasmids of fungi and plants. -
Emerging Viral Diseases of Fish and Shrimp Peter J
Emerging viral diseases of fish and shrimp Peter J. Walker, James R. Winton To cite this version: Peter J. Walker, James R. Winton. Emerging viral diseases of fish and shrimp. Veterinary Research, BioMed Central, 2010, 41 (6), 10.1051/vetres/2010022. hal-00903183 HAL Id: hal-00903183 https://hal.archives-ouvertes.fr/hal-00903183 Submitted on 1 Jan 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Vet. Res. (2010) 41:51 www.vetres.org DOI: 10.1051/vetres/2010022 Ó INRA, EDP Sciences, 2010 Review article Emerging viral diseases of fish and shrimp 1 2 Peter J. WALKER *, James R. WINTON 1 CSIRO Livestock Industries, Australian Animal Health Laboratory (AAHL), 5 Portarlington Road, Geelong, Victoria, Australia 2 USGS Western Fisheries Research Center, 6505 NE 65th Street, Seattle, Washington, USA (Received 7 December 2009; accepted 19 April 2010) Abstract – The rise of aquaculture has been one of the most profound changes in global food production of the past 100 years. Driven by population growth, rising demand for seafood and a levelling of production from capture fisheries, the practice of farming aquatic animals has expanded rapidly to become a major global industry. -
2008.005I (To Be Completed by ICTV Officers)
Taxonomic proposal to the ICTV Executive Committee This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). Code(s) assigned: 2008.005I (to be completed by ICTV officers) Short title: Creation of a new species in the genus, Cripavirus, family Dicistroviridae (e.g. 6 new species in the genus Zetavirus; re-classification of the family Zetaviridae etc.) Modules attached 1 2 3 4 5 (please check all that apply): 6 7 Author(s) with e-mail address(es) of the proposer: Dicistroviridae Study Group: Nobuhiko Nakashima ([email protected]), Karyn Johnson ([email protected]); Frank van der Wilk ([email protected]); Les Domier: ([email protected]); Peter Christian ([email protected]); Judy Chen ([email protected]) ; Tamas Bakonyi ([email protected]). ICTV-EC or Study Group comments and response of the proposer: MODULE 5: NEW SPECIES Code 2008.005I (assigned by ICTV officers) To create Homalodisca coagulata virus-1, a new species assigned as follows: Fill in all that apply. Ideally, species Genus: Cripavirus should be placed within a genus, but Subfamily: it is acceptable to propose a species Family: Dicistroviridae that is within a Subfamily or Family Order: Picornavirales but not assigned to an existing genus (in which case put “unassigned” in the genus box) Name(s) of proposed new species: Homalodisca coagulata virus-1 Argument to justify the creation of the new species: If the species are to be assigned to an existing genus, list the criteria for species demarcation and explain how the proposed members meet these criteria. -
Arxiv:2102.00316V2 [Q-Bio.SC] 8 Apr 2021 Dependent RNA-Polymerase (Abbreviated As Rdrp) [2]
Polysomally Protected Viruses Michael Wilkinson1;2, David Yllanes1 and Greg Huber1 1 Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA 2 School of Mathematics and Statistics, The Open University,Walton Hall, Milton Keynes, MK7 6AA, UK E-mail: [email protected] January 2021 Abstract. It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and how its presence might be detected by ribosome profiling. There are two possible forms for such a polysomally protected virus, depending upon whether just the forward strand or both the forward and complementary strands can be encased by ribosomes (these will be termed type 1 and type 2, respectively). It is argued that in the type 2 case the viral RNA would evolve an ambigrammatic property, whereby the viral genes are free of stop codons in a reverse reading frame (with forward and reverse codons aligned). Recent observations of ribosome profiles of ambigrammatic narnavirus sequences are consistent with our predictions for the type 2 case. 1. Introduction A canonical model for the structure of a virus [1] consists of genetic material encased in a capsid composed of a protein shell. A simpler model has also been observed, termed a narnavirus (this term is a contraction of `naked RNA virus'). The narnavirus examples that have been characterised appear to be single genes, which code for an RNA- arXiv:2102.00316v2 [q-bio.SC] 8 Apr 2021 dependent RNA-polymerase (abbreviated as RdRp) [2]. -
1 Studies on Two Genomic Variants of Taura
Studies on Two Genomic Variants of Taura Syndrome Virus: Infection under Hyperthermic Conditions and Detection with a Novel Monoclonal Antibody Item Type text; Electronic Dissertation Authors Cote, Isabelle Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 09/10/2021 11:46:35 Link to Item http://hdl.handle.net/10150/195556 1 STUDIES ON TWO GENOMIC VARIANTS OF TAURA SYNDROME VIRUS: INFECTION UNDER HYPERTHERMIC CONDITIONS AND DETECTION WITH A NOVEL MONOCLONAL ANTIBODY by Isabelle Côté __________________________________ A Dissertation Submitted to the Faculty of the DEPARTMENT OF VETERINARY SCIENCE AND MICROBIOLOGY In Partial Fulfilment of the Requirements For the Degree of DOCTOR OF PHILOSPHY WITH A MAJOR IN MICROBIOLOGY In the Graduate College THE UNIVERSITY OF ARIZONA 2008 2 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Isabelle Côté entitled: "Studies on Two Genomic Variants of Taura Syndrome Virus: Infection under Hyperthermic Conditions and Detection with a Novel Monoclonal Antibody” and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy. _______________________________________________ Date: __06/09/2008_______ Donald V. Lightner, Ph.D. _______________________________________________ Date: __06/09/2008_______ Bonnie T. Poulos, Ph.C. _______________________________________________ Date: __06/09/2008_______ Michael A. Cusanovich, Ph.D. _______________________________________________ Date: __06/09/2008_______ Carol L. -
Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses
viruses Article Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses Thanuja Thekke-Veetil 1, Doris Lagos-Kutz 2 , Nancy K. McCoppin 2, Glen L. Hartman 2 , Hye-Kyoung Ju 3, Hyoun-Sub Lim 3 and Leslie. L. Domier 2,* 1 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; [email protected] 2 Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; [email protected] (D.L.-K.); [email protected] (N.K.M.); [email protected] (G.L.H.) 3 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; [email protected] (H.-K.J.); [email protected] (H.-S.L.) * Correspondence: [email protected]; Tel.: +1-217-333-0510 Academic Editor: Eugene V. Ryabov and Robert L. Harrison Received: 5 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
ICTV Code Assigned: 2011.001Ag Officers)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . -
High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage
Edinburgh Research Explorer High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage Citation for published version: Ng, TF, Marine, R, Wang, C, Simmonds, P, Kapusinszky, B, Bodhidatta, L, Oderinde, BS, Wommack, KE & Delwart, E 2012, 'High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage', Journal of Virology, vol. 86, no. 22, pp. 12161-12175. https://doi.org/10.1128/jvi.00869-12 Digital Object Identifier (DOI): 10.1128/jvi.00869-12 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Journal of Virology Publisher Rights Statement: Copyright © 2012, American Society for Microbiology. All Rights Reserved. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage Terry Fei Fan Ng,a,b Rachel Marine,c Chunlin Wang,d Peter Simmonds,e Beatrix Kapusinszky,a,b Ladaporn Bodhidatta,f Bamidele Soji Oderinde,g K. -
Meta-Transcriptomic Detection of Diverse and Divergent RNA Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.141184; this version posted June 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Meta-transcriptomic detection of diverse and divergent 2 RNA viruses in green and chlorarachniophyte algae 3 4 5 Justine Charon1, Vanessa Rossetto Marcelino1,2, Richard Wetherbee3, Heroen Verbruggen3, 6 Edward C. Holmes1* 7 8 9 1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 10 Environmental Sciences and School of Medical Sciences, The University of Sydney, 11 Sydney, Australia. 12 2Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical 13 Research, Westmead, NSW 2145, Australia. 14 3School of BioSciences, University of Melbourne, VIC 3010, Australia. 15 16 17 *Corresponding author: 18 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 19 Environmental Sciences and School of Medical Sciences, 20 The University of Sydney, 21 Sydney, NSW 2006, Australia. 22 Tel: +61 2 9351 5591 23 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.141184; this version posted June 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.